8V08

Crystal structure of human PLD4 co-crystallized with 5'Pi-ssDNA

  • Classification: HYDROLASE/DNA
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2023-11-17 Released: 2024-03-13 
  • Deposition Author(s): Yuan, M., Wilson, I.A.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute on Aging (NIH/NIA)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.266 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and mechanistic insights into disease-associated endolysosomal exonucleases PLD3 and PLD4.

Yuan, M.Peng, L.Huang, D.Gavin, A.Luan, F.Tran, J.Feng, Z.Zhu, X.Matteson, J.Wilson, I.A.Nemazee, D.

(2024) Structure 32: 766-779.e7

  • DOI: https://doi.org/10.1016/j.str.2024.02.019
  • Primary Citation of Related Structures:  
    8V05, 8V06, 8V07, 8V08

  • PubMed Abstract: 

    Endolysosomal exonucleases PLD3 and PLD4 (phospholipases D3 and D4) are associated with autoinflammatory and autoimmune diseases. We report structures of these enzymes, and the molecular basis of their catalysis. The structures reveal an intra-chain dimer topology forming a basic active site at the interface. Like other PLD superfamily members, PLD3 and PLD4 carry HxKxxxxD/E motifs and participate in phosphodiester-bond cleavage. The enzymes digest ssDNA and ssRNA in a 5'-to-3' manner and are blocked by 5'-phosphorylation. We captured structures in apo, intermediate, and product states and revealed a "link-and-release" two-step catalysis. We also unexpectedly demonstrated phosphatase activity via a covalent 3-phosphohistidine intermediate. PLD4 contains an extra hydrophobic clamp that stabilizes substrate and could affect oligonucleotide substrate preference and product release. Biochemical and structural analysis of disease-associated mutants of PLD3/4 demonstrated reduced enzyme activity or thermostability and the possible basis for disease association. Furthermore, these findings provide insight into therapeutic design.


  • Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: myuan@scripps.edu.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5'-3' exonuclease PLD4488Homo sapiensMutation(s): 0 
Gene Names: PLD4C14orf175UNQ2488/PRO5775
EC: 3.1.16.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96BZ4 (Homo sapiens)
Explore Q96BZ4 
Go to UniProtKB:  Q96BZ4
PHAROS:  Q96BZ4
GTEx:  ENSG00000166428 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96BZ4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
5'-3' exonuclease PLD4488Homo sapiensMutation(s): 0 
Gene Names: PLD4C14orf175UNQ2488/PRO5775
EC: 3.1.16.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96BZ4 (Homo sapiens)
Explore Q96BZ4 
Go to UniProtKB:  Q96BZ4
PHAROS:  Q96BZ4
GTEx:  ENSG00000166428 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96BZ4
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
ssDNA
C, D
3Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
NEP
Query on NEP
A
L-PEPTIDE LINKINGC6 H10 N3 O5 PHIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.266 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.98α = 90
b = 88.98β = 90
c = 273.968γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI142945
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesAG070775

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release
  • Version 1.1: 2024-04-17
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Database references